config.py

path = "data/130723_data_hepatocytes.h5ad"

# small set of genes
central = [
    "Oat",
    "Cyp2e1",
    "Lect2",
    "Cyp2c37",
    "Gulo",
    "Cyp2a5",
    "Glul",
    "Aldh1a1",
    "Cyp1a2",
    "Slc22a1",
    "Slc1a2",
]
portal = ["Pck1", "Aldh1b1", "Ctsc", "Sds", "Hal", "Hsd17b13", "Cyp2f2"]


# full set of genes
central_big = [
    "Rnase4",
    "Glul",
    "Oat",
    "Cyp2c37",
    "Airn",
    "Lect2",
    "Slc22a1",
    "Cyp2e1",
    "Cyp7a1",
    "Gm30117",
    "Aldh1a1",
    "Cyp2c50",
    "Lhpp",
    "Cyp1a2",
    "Slc1a2",
    "Cyp2a5",
    "Pon1",
    "Slco1b2",
    "Cyp2c54",
    "Mgst1",
    "Gulo",
    "Lgr5",
]

portal_big = [
    "Ctsc",
    "Aldh1b1",
    "Pigr",
    "Serpina1d",
    "Apoc2",
    "Hal",
    "Gc",
    "Hsd17b13",
    "Itih4",
    "Apoc3",
    "Hpx",
    "Hsd17b6",
    "Apoa4",
    "Sds",
    "Serpina1b",
    "Serpinc1",
    "Alb",
    "Cyp2f2",
    "Pck1",
]

genes = central + portal
genes_big = central_big + portal_big

clamp_gene = "Cyp2e1"  # gene to clamp

# training parameters
batch_size = 0  # batch size, put zero for full batch
n_iter = 10000  # number of iterations

# name of the output files
save = False
name = "big_set"